DeltaBreed Example

QBMS

This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like EBS, BMS, BreedBase, and GIGWA (using BrAPI calls). Extra helper functions support environmental data sources, including TerraClimate and FAO HWSDv2 soil database.

DeltaBreed

DeltaBreed is an open source data management software for specialty crop and animal breeders. It is developed by Breeding Insight with funding from the U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS) through Cornell University.

The easiest way to try DeltaBreed is to use their public sandbox. The User Manual, which describes how to use DeltaBreed’s features, may be viewed here.

The easiest way to test the QBMS integration with DeltaBreed is to use their public sandbox. The DeltaBreed user documentation is available here.

Please note:

  • All submitted data are public; do not submit private data on the public sandbox.
  • The public sandbox database is routinely reset and submitted data may be removed without notice.
  • Access tokens should be treated as credentials and should not be committed to source code or shared publicly.

Accessing DeltaBreed Sandbox:

Open the DeltaBreed public sandbox. The sandbox landing page displays the guest account credentials that can be used to explore the available demonstration data.

Click “LOG IN” beside the guest account information. DeltaBreed will redirect you to the ORCID authentication page. Then, click “SIGN IN with ORCID” and use the sandbox guest credentials shown on the DeltaBreed landing page. After authentication, you will be redirected back to DeltaBreed and logged into the “Public Sandbox” breeding program. To obtain the required BrAPI connection information:

  1. Select “BrAPI” from the sidebar menu.
  2. Open the “BrAPI Base URL” tab.
  3. Copy the displayed BrAPI base URL.
  4. Click “Generate Access Token”.
  5. Copy the generated token for use in the current QBMS session.

BrAPI

The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. This community driven standard is free to be used by anyone interested in plant breeding data management.

Example

# load the QBMS library
library(QBMS)

# DeltaBreed BrAPI Base URL
brapi_base_url <- 'https://sandbox.breedinginsight.net/v1/programs/ef0a5341-53d1-41b3-aeae-90692f9d563d'

# config the EBS connection
set_qbms_config(url = brapi_base_url, engine = 'deltabreed')

# set your generated access token manually
set_token(readline('token:'))

# get the list of crops
list_crops()

# list all breeding programs in the selected crop
list_programs()

# select a breeding program by name
set_program("Public Sandbox")

# list all studies/trials in the selected program
list_trials()

# select a specific study/trial by name
set_trial("2025 Disease Screen ABCD")

# list all environments/locations information in the selected study/trial
list_studies()

# select a specific environment/location by name
set_study("Win23")

# retrieve general information, data, and germplasm list 
# of the selected environment/location
info <- get_study_info()
data <- get_study_data()
# germplasm <- get_germplasm_list()

# get observation variable ontology in the selected study/trial
ontology <- get_trial_obs_ontology()

# retrieve multi-environment trial data of the selected study/trial
MET <- get_trial_data()

Using the Connection Wizard

Alternatively, the DeltaBreed connection can be configured interactively using the Connection Wizard:

library(QBMS)

result <- qbms_wizard()

In the wizard, select DeltaBreed, enter the BrAPI base URL, and paste the access token generated from the DeltaBreed BrAPI page. After selecting the required program, trial, and study, the QBMS session is ready for data retrieval:

study_data <- get_study_data()

For details on using the wizard from the R console, Shiny applications, or interactive R Markdown documents, see the Connection Wizard vignette/article.